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- PDB-1onm: Solution Structure of a DNA duplex containing A:G mismatch. d(GCT... -

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Basic information

Entry
Database: PDB / ID: 1onm
TitleSolution Structure of a DNA duplex containing A:G mismatch. d(GCTTCAGTCGT):d(ACGACGGAAGC)
Components
  • 5'-D(*AP*CP*GP*AP*CP*GP*GP*AP*AP*GP*C)-3'
  • 5'-D(*GP*CP*TP*TP*CP*AP*GP*TP*CP*GP*T)-3'
KeywordsDNA / A/G mismatch / A:G mismatch / A/G mispair / A:G mispair
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / Total Relaxation Matrix, Molecular Dynamics were used.
AuthorsSanchez, A.M. / Volk, D.E. / Gorenstein, D.G. / Lloyd, R.S.
CitationJournal: DNA REPAIR / Year: 2003
Title: Initiation of repair of A/G mismatches is modulated by sequence context
Authors: Sanchez, A.M. / Volk, D.E. / Gorenstein, D.G. / Lloyd, R.S.
History
DepositionFeb 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*GP*CP*TP*TP*CP*AP*GP*TP*CP*GP*T)-3'
B: 5'-D(*AP*CP*GP*AP*CP*GP*GP*AP*AP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)6,7322
Polymers6,7322
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10all calculated structures submitted
RepresentativeModel #1all equally representative

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Components

#1: DNA chain 5'-D(*GP*CP*TP*TP*CP*AP*GP*TP*CP*GP*T)-3'


Mass: 3340.183 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*AP*CP*GP*AP*CP*GP*GP*AP*AP*GP*C)-3'


Mass: 3392.238 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2112D NOESY
1222D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM DNA duplex; 25 mM phosphate, 50 mM NaCl, 1 mM EDTA;90% H2O/10% D2O
21 mM DNA duplex; 25 mM phosphate, 50 mM NaCl, 1 mM EDTA;99.96% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
125 mM Phosphate,50 mM NaCl 6.8 ambient 283 K
225 mM Phosphate,50 mM NaCl 6.8 ambient 288 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS6001
Varian UNITYPLUSVarianUNITYPLUS7502

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Varian, Inc.processing
MORASS2.51Gorenstein, D.G. et al.iterative matrix relaxation
Amber5Case, D.A. et al.refinement
RefinementMethod: Total Relaxation Matrix, Molecular Dynamics were used.
Software ordinal: 1
Details: 624 total restraints were used: 500 derived from 2D NOE data and 124 dihedral angle restraints.
NMR representativeSelection criteria: all equally representative
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 10 / Conformers submitted total number: 10

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